Variant report

Variant	rs7527939
Chromosome Location	chr1:210536025-210536026
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:210405867..210408909-chr1:210535692..210538632,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082497	Chromatin interaction
ENSG00000203706	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10489388	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12729428	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17016026	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17759021	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2357583	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3765872	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3765879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3765884	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs60935759	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61828656	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6540589	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6656628	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6656669	0.83[CEU][hapmap]
rs6669428	0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6677509	0.89[CEU][hapmap]
rs6690120	0.88[CEU][hapmap]
rs7354957	0.85[EUR][1000 genomes]
rs7355019	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs742560	0.89[CEU][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.82[EUR][1000 genomes]
rs7530104	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs7550408	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7550554	0.89[CEU][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs761171	0.88[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	23142968	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7527939	PLXNA2	cis	parietal	SCAN
rs7527939	ELK4	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210503600-210546800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:210513000-210540400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:210522600-210537600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:210525200-210538000	Weak transcription	Ovary	ovary
5	chr1:210528400-210536600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:210529600-210586000	Weak transcription	Pancreas	Pancrea
7	chr1:210532400-210540200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:210532400-210545800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:210532600-210540200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:210533200-210537800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:210533200-210540800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:210534200-210536800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:210534400-210536200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:210534400-210536200	Enhancers	HSMM	muscle
15	chr1:210534400-210536600	Enhancers	Fetal Heart	heart
16	chr1:210534400-210536800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:210534400-210536800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr1:210534400-210536800	Enhancers	NHLF	lung
19	chr1:210534400-210536800	Enhancers	Osteobl	bone
20	chr1:210534600-210536400	Weak transcription	Stomach Mucosa	stomach
21	chr1:210534600-210537600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:210534600-210538800	Enhancers	Brain Cingulate Gyrus	brain
23	chr1:210534600-210541800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr1:210534600-210546800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:210534800-210536400	Weak transcription	Adipose Nuclei	Adipose
26	chr1:210534800-210536600	Weak transcription	Small Intestine	intestine
27	chr1:210534800-210536600	Weak transcription	A549	lung
28	chr1:210534800-210536800	Enhancers	Liver	Liver
29	chr1:210534800-210537400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:210534800-210537400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:210534800-210537600	Weak transcription	Fetal Kidney	kidney
32	chr1:210534800-210537800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:210534800-210538000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:210534800-210538000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:210534800-210538000	Weak transcription	Esophagus	oesophagus
36	chr1:210534800-210538000	Weak transcription	Thymus	Thymus
37	chr1:210534800-210539400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:210534800-210540000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:210534800-210540000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr1:210534800-210540000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:210534800-210540000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:210534800-210540200	Weak transcription	Fetal Brain Male	brain
43	chr1:210534800-210543000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:210534800-210543000	Weak transcription	Right Atrium	heart
45	chr1:210535000-210536200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr1:210535000-210536200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:210535000-210536800	Enhancers	HSMMtube	muscle
48	chr1:210535000-210537400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:210535000-210539800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:210535000-210540000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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